Waterlogging, like other abiotic stresses, severely inhibits the growth and development of watermelon. However, few genes conferring waterlogging escape response have been identified in this crop to date. In this study, we performed bulked segregant analysis on a F₂ population exhibiting significant variation in waterlogging-induced shoot elongation. A 6.59 Mb candidate region on chromosome 7 was identified to be associated with waterlogging-induced shoot elongation. Integrated resequencing, fine-mapping and transcriptome analyses indicated that Cla97C07G134400 (ClSCPL50) candidate gene associated with waterlogging-induced shoot elongation. These findings provide novel insights into the genetic basis of the waterlogging escape response in watermelon and identify a potential target gene for improving waterlogging escape response in other dryland crops.